Structural and Functional Studies of an Intermediate on the Pathway to Operator Binding by Escherichia coli MetJ
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- 作者：He ; Yi-Yuan ; Garvie ; Colin W. ; Elworthy ; Stone ; Manfield ; Iain W. ; McNally ; Teresa ; Lawrenson ; Isobel D. ; et. al.
- 关键词：methionine repressor ; crystal structure ; operator complex intermediate ; AdoMet ; S-adenosylmethionine ; EMSA ; electrophoretic mobility shift assays
- 刊名：Journal of Molecular Biology
- 出版年：2002
- 出版时间：June 28, 2002
- 年：2002
- 卷：320
- 期：1
- 页码：39-53
- 全文大小：743 K
文摘
We present the results of in vitro DNA-binding assays for a mutant protein (Q44K) of the E.coli methionine repressor, MetJ, as well as the crystal structure at 2.2Å resolution of the apo-mutant bound to a 10-mer oligonucleotide encompassing an 8bp met-box sequence. The wild-type protein binds natural operators co-operatively with respect to protein concentration forming at least a dimer of repressor dimers along operator DNAs. The minimum operator length is thus 16bp, each MetJ dimer interacting with a single met-box site. In contrast, the Q44K mutant protein can also bind stably as a single dimer to 8bp target sites, in part due to additional contacts made to the phosphodiester backbone outside the 8bp target via the K44 side-chains. Protein–protein co-operativity in the mutant is reduced relative to the wild-type allowing the properties of an intermediate on the pathway to operator site saturation to be examined for the first time. The crystal structure of the decamer complex shows a unique conformation for the protein bound to the single met-box site, possibly explaining the reduced protein–protein co-operativity. In both the extended and minimal DNA complexes formed, the mutant protein makes slightly different contacts to the edges of DNA base-pairs than the wild-type, even though the site of amino acid substitution is distal from the DNA-binding motif. Quantitative binding assays suggest that this is not due to artefacts caused by the crystallisation conditions but is most likely due to the relatively small contribution of such direct contacts to the overall binding energy of DNA–protein complex formation, which is dominated by sequence-dependent distortions of the DNA duplex and by the protein–protein contact between dimers.